Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of CNA associated with bone metastatic breast cancer cells

ABSTRACT: We used comparative genomic hybridization (CGH) analysis between Bone metastatic derivatives isolated in vivo and parental cells and focused on genomic changes affecting the expression of potential bone metastasis. Total RNA from biological and technical replicates of parental MCF7 and BoM2 bone metastasis derivatives grown for 48 hours in regular media (see growth protocol). High-molecular DNA was isolated from in vitro cultured MCF7 and BoM2 cells using GeneEluteM-bM-^DM-" Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) following manufactureM-bM-^@M-^Ys instructions.

ORGANISM(S): Homo sapiens

SUBMITTER: Evarist Letschert

PROVIDER: E-GEOD-51237 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Isolation and in vitro expansion of human colonic stem cells [CGH]

Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations. Analysis of chromosomal stability of colonic tissue or in vitro-cultured organoids via comparison with blood cells derived from the same individual.

2011-11-22 | E-GEOD-31256 | biostudies-arrayexpress

16q22-24 DNA amplification specifically predicts and mediates, through MAF gene, breast cancer bone metastasis.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-01 | E-GEOD-51238 | biostudies-arrayexpress

Isolation and in vitro expansion of human colonic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE31255: Isolation and in vitro expansion of human colonic stem cells [Expression profile] GSE31256: Isolation and in vitro expansion of human colonic stem cells [CGH] Refer to individual Series

2011-11-22 | E-GEOD-31257 | biostudies-arrayexpress

Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea

Project description:Reuse of materials in DNA hybridization based methods has been known since the advent of Southern membranes. Array based comparative genomic hybridization is essentially Southern hybridization with multiple probes immobilized on a solid surface. We have shown that comparative genomic hybridization microarrays fabricated with maskless array synthesizer technology can be used up to four times with application of 1,3-dimethylurea as array-stripping agent. We reproducibly detected chromosomal aberrations, 0.6 to 22.4 Mb in size, in four hybridization rounds using regenerated microarray slides. We have also demonstrated that regenerated arrays can detect smaller alterations, 16 M-bM-^@M-^S 200 kbp, such as common copy number variants, as well as complex aberration profiles in tumor. Peripheral blood leukocyte DNA samples from 7 individuals with subchromosomal aberrations vs a pool of female DNA (Promega). The experiments were performed in quadruplicate on succesively regenerated microarrays. One dye swap was performed..

2012-05-22 | E-GEOD-35740 | biostudies-arrayexpress

Identification of global copy number variations among diverse pig breeds by a CGH array

Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0). In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).

2013-08-09 | E-GEOD-41488 | biostudies-arrayexpress

Genomic profiling of human Tert/shp53/Ras mesenchymal cells isolated from several xenografted tumors and their non-transformant epithelial counterparts

Project description:The epithelial-mesenchymal transition (EMT) is an embryonic transdifferentiation program which consists of the conversion of polarized epithelial cells into a motile mesenchymal phenotype. EMT is aberrantly reactivated during tumor progression, promoting metastatic dissemination. Herein, we demonstrate that EMT-permissive conditions also favor tumor initiation by minimizing the number of events required for neoplastic transformation. We further demonstrated that even the partial commitment of human mammary epithelial cells into an EMT program is sufficient to confer malignant properties, suggesting that the reactivation of embryonic EMT inducers participates to the primary tumor growth long before the initiation of the invasion-metastasis cascade. arrayCGH profiles analysis of Tert/shp53/Ras epithelial HMEC derivatives and 3 different tumors generated after injection of mesenchymal Tert/shp53/Ras/ HMEC derivatives in fad pads of nude mice

2011-01-11 | E-GEOD-26534 | biostudies-arrayexpress

Comparative genomic hybridization by array of E. coli strains CFT073, Nissle 1917 and ABU 83872

Project description:CGH analysis of CFT073, Nissle 1917 and ABU 83972

2010-06-09 | E-MTAB-212 | biostudies-arrayexpress

methylation_selmi

Project description:DNA and RNA collection of identical and non identical twins with Primary biliary cirrhosis (PBC) and performed a genome-wide investigation to determine differences in DNA methylation, CNV, and gene. PBC compared to healthy patient. 998 X chromosome and 18,086 randomly selected autosomal chromosome promoter sites (Roche Nimblegen, Madison, WI. in situ oligonucleotide hybridizatio.

2014-02-26 | E-MTAB-2343 | biostudies-arrayexpress

DamID profiling of neural transcription factor (Abrupt and Knot) binding in Drosophila melanogaster embryos

Project description:Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits. Each Dam-fusion-derived sample is compared to a control Dam-only sample. Four biological replicates were performed.

2013-11-27 | E-GEOD-38659 | biostudies-arrayexpress

T (Brachyury) gene duplication confers major susceptibility to familial chordoma

Project description:Using high-resolution array-CGH, we identified unique duplications of a region on 6q27 in four multiplex (≥ with ≥ 3 cases) families of chordoma, a cancer of presumed notochordal origin. comparison of test samples from chordoma families to a reference DNA sample

2009-10-04 | E-GEOD-17668 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data